ambit2.some

Class SOMEShell

java.lang.Object

ambit2.base.external.CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

ambit2.some.SOMEShell

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

public class SOMEShell
extends CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Wrapper for Site Of Metabolism Estimator (SOME) http://www.dddc.ac.cn/adme/myzheng/SOME_1_0.tar.gz. Expects SOME executable as set by the SOME_HOME environment var.

Author:

nina

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected String	inFile
protected String[]	outFile
static String	SOME_HOME
static String	SOME_RESULT
protected boolean	useOriginalStructure

Fields inherited from class ambit2.base.external.CommandShell

enabled, executables, exitCode, inputFile, logger, os_FreeBSD, os_LINUX, os_LINUX64, os_MAC, os_WINDOWS, os_WINDOWS7, os_WINDOWSVISTA, outputFile, prefix, runAsync, workFolder

Constructor Summary

Constructors

Constructor and Description
SOMEShell()

Method Summary

Modifier and Type	Method and Description
protected boolean	canApply(org.openscience.cdk.interfaces.IAtomContainer atomcontainer)
protected String	getHomeDir(File file)
protected String	getPath(File file)
protected void	initialize()
boolean	isUseOriginalStructure()
protected org.openscience.cdk.interfaces.IAtomContainer	parseOutput(String mopac_path, org.openscience.cdk.interfaces.IAtomContainer mol) Does nothing, override with smth meaningfull
protected List<String>	prepareInput(String path, org.openscience.cdk.interfaces.IAtomContainer mol) Returns empty string, override with smth meaningfull
org.openscience.cdk.interfaces.IAtomContainer	process(org.openscience.cdk.interfaces.IAtomContainer target)
org.openscience.cdk.interfaces.IAtomContainer	runShell(org.openscience.cdk.interfaces.IAtomContainer mol)
void	setUseOriginalStructure(boolean useOriginalStructure)
String	toString()
protected org.openscience.cdk.interfaces.IAtomContainer	transform_input(org.openscience.cdk.interfaces.IAtomContainer mol)
protected org.openscience.cdk.interfaces.IAtomContainer	transform(org.openscience.cdk.interfaces.IAtomContainer mol)

Methods inherited from class ambit2.base.external.CommandShell

addExecutable, addExecutable, addExecutableFreeBSD, addExecutableLinux, addExecutableLinux64, addExecutableMac, addExecutableWin, close, exitCodeOK, getExecutable, getExecutable, getExitCode, getHomeFromConfig, getID, getInputFile, getMsgemptymolecule, getOutputFile, getWorkFolder, isEnabled, open, parseOutput, processStdOut, runShell, setEnabled, setExitCode, setInputFile, setOutputFile, setWorkFolder, transform

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

SOME_RESULT

public static final String SOME_RESULT

See Also:

Constant Field Values

SOME_HOME

public static final String SOME_HOME

See Also:

Constant Field Values

useOriginalStructure

protected boolean useOriginalStructure

inFile

protected String inFile

outFile

protected String[] outFile

Constructor Detail

SOMEShell

public SOMEShell()
          throws ShellException

Throws:

ShellException

Method Detail

isUseOriginalStructure

public boolean isUseOriginalStructure()

setUseOriginalStructure

public void setUseOriginalStructure(boolean useOriginalStructure)

getHomeDir

protected String getHomeDir(File file)

Overrides:

getHomeDir in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

initialize

protected void initialize()
                   throws ShellException

Overrides:

initialize in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Throws:

ShellException

transform_input

protected org.openscience.cdk.interfaces.IAtomContainer transform_input(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                                 throws ShellException

Overrides:

transform_input in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Throws:

ShellException

getPath

protected String getPath(File file)

Overrides:

getPath in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

prepareInput

protected List<String> prepareInput(String path,
                                    org.openscience.cdk.interfaces.IAtomContainer mol)
                             throws ShellException

Description copied from class: CommandShell

Returns empty string, override with smth meaningfull

Overrides:

prepareInput in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Returns:

list of command line parameters (exe name excluded) to be passed to the executable

Throws:

ShellException

parseOutput

protected org.openscience.cdk.interfaces.IAtomContainer parseOutput(String mopac_path,
                                                                    org.openscience.cdk.interfaces.IAtomContainer mol)
                                                             throws ShellException

Description copied from class: CommandShell

Does nothing, override with smth meaningfull

Specified by:

parseOutput in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Throws:

ShellException

transform

protected org.openscience.cdk.interfaces.IAtomContainer transform(org.openscience.cdk.interfaces.IAtomContainer mol)

Specified by:

transform in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

runShell

public org.openscience.cdk.interfaces.IAtomContainer runShell(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                       throws ShellException

Overrides:

runShell in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Throws:

ShellException

canApply

protected boolean canApply(org.openscience.cdk.interfaces.IAtomContainer atomcontainer)
                    throws ShellException

Throws:

ShellException

toString

public String toString()

Overrides:

toString in class Object

process

public org.openscience.cdk.interfaces.IAtomContainer process(org.openscience.cdk.interfaces.IAtomContainer target)
                                                      throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

process in interface net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Overrides:

process in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Throws:

net.idea.modbcum.i.exceptions.AmbitException